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From Xiayuan Huang <huan...@cs.wisc.edu>
Subject RE: Resource Initialization Exception cTAKES 3.1.1
Date Mon, 17 Mar 2014 21:48:58 GMT
Hello Pei,

I met the similar exception, I tried to solve it for long but still cnt 
figure it out. Could you please have a look?



3/17/14 4:10:14 PM - 15: 
org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: 
Exception occurred
org.apache.uima.resource.ResourceInitializationException
	at 
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
	at 
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
	at 
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
	at 
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
	at 
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
	at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
	at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
	at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
	at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
	at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
	at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
	at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
	at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
	at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
	at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
	at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
	at 
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
	at 
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
	at 
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
	at 
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
	at 
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at 
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at 
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
	at 
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
	at java.awt.Component.processMouseEvent(Component.java:6505)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
	at java.awt.Component.processEvent(Component.java:6270)
	at java.awt.Container.processEvent(Container.java:2229)
	at java.awt.Component.dispatchEventImpl(Component.java:4861)
	at java.awt.Container.dispatchEventImpl(Container.java:2287)
	at java.awt.Component.dispatchEvent(Component.java:4687)
	at 
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
	at 
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
	at java.awt.Container.dispatchEventImpl(Container.java:2273)
	at java.awt.Window.dispatchEventImpl(Window.java:2719)
	at java.awt.Component.dispatchEvent(Component.java:4687)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
	at java.awt.EventQueue.access$200(EventQueue.java:103)
	at java.awt.EventQueue$3.run(EventQueue.java:682)
	at java.awt.EventQueue$3.run(EventQueue.java:680)
	at java.security.AccessController.doPrivileged(Native Method)
	at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
	at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.awt.EventQueue$4.run(EventQueue.java:696)
	at java.awt.EventQueue$4.run(EventQueue.java:694)
	at java.security.AccessController.doPrivileged(Native Method)
	at 
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
	at 
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:244)
	at 
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:163)
	at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)
	at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147)
	at 
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:97)
Caused by: java.io.FileNotFoundException: 
org/apache/ctakes/dictionary/lookup/rxnorm_index
	at 
org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:93)
	at 
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:68)
	at 
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
	... 58 more




On 2014-03-13 11:22, Measure, Alex - BLS wrote:
> Thanks Pei. I did that previously, but I redid it again per your
> instructions and everything works perfectly now. I must have made an
> error. Thanks!
> 
> Alex
> 
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Thursday, March 13, 2014 11:59 AM
> To: user@ctakes.apache.org
> Subject: RE: Resource Initialization Exception cTAKES 3.1.1
> 
> From the downloads page, have you tried:
> Resources
> Resources are required to run most of cTAKES. They are available for
> download from SourceForge: ctakes-resources-3.1.0.zip [1].
> Please download, unzip and add/merge the contents to the existing
> resources directory. Follow the User or Developer Install Guide to
> direct you through the installation process.
> [1]
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
> 
> From: Measure, Alex - BLS [mailto:Measure.Alex@bls.gov]
> Sent: Thursday, March 13, 2014 11:53 AM
> To: 'user@ctakes.apache.org'
> Subject: Resource Initialization Exception cTAKES 3.1.1
> 
> I am trying to resolve a Resource Initialization Exception I am
> receiving while loading the AggregatePlaintextUMLSProcessor, can
> anyone assist me? Details are below:
> 
> I am using ctakes-3.1.1 along with ctakes-resources-3.1.0, installed
> per the User Guide on a Windows 7 machine. I have entered my UMLS
> license information in the CVD.bat file and increased the max heap
> size to 4096M (my machine has 8GB of memory).
> 
> When I attempt to load the AggregatePlaintextUMLSProcessor in the CVD
> I receive a Resource Initialization Exception. I have no trouble
> loading and running the AggregatePlaintextProcessor. I also have no
> trouble using the AggregatePlaintextUMLSProcessor with an earlier
> version of ctakes, ctakes-3.0-incubating.
> 
> If I look at the command prompt as the CVD is attempting to load the
> Processor, it appears to be getting stuck at:
> 
> Loading model:
> .............................
> 13 Mar 2014 11:38:36  INFO Chunker - Chunker model file:
> C:\Users\measure_a\Desktop\apache
> -ctakes-3.1.1\apache-ctakes-3.1.1\resources\org\apache\ctakes\chunker\models\chunker-model
> .zip
> 
> 
> The full log file is below:
> 3/13/14 11:38:36 AM - 14:
> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
> Exception occurred
> org.apache.uima.resource.ResourceInitializationException
>                 at
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
>                 at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
>                 at
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>                 at
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>                 at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
>                 at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
>                 at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>                 at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>                 at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>                 at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>                 at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>                 at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>                 at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>                 at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>                 at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>                 at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>                 at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>                 at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
>                 at
> org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>                 at
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
>                 at
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
>                 at
> javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>                 at
> javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>                 at
> javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>                 at javax.swing.DefaultButtonModel.setPressed(Unknown 
> Source)
>                 at javax.swing.AbstractButton.doClick(Unknown Source)
>                 at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>                 at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
> Source)
>                 at java.awt.Component.processMouseEvent(Unknown Source)
>                 at javax.swing.JComponent.processMouseEvent(Unknown 
> Source)
>                 at java.awt.Component.processEvent(Unknown Source)
>                 at java.awt.Container.processEvent(Unknown Source)
>                 at java.awt.Component.dispatchEventImpl(Unknown Source)
>                 at java.awt.Container.dispatchEventImpl(Unknown Source)
>                 at java.awt.Component.dispatchEvent(Unknown Source)
>                 at
> java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>                 at
> java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>                 at java.awt.LightweightDispatcher.dispatchEvent(Unknown

> Source)
>                 at java.awt.Container.dispatchEventImpl(Unknown Source)
>                 at java.awt.Window.dispatchEventImpl(Unknown Source)
>                 at java.awt.Component.dispatchEvent(Unknown Source)
>                 at java.awt.EventQueue.dispatchEventImpl(Unknown 
> Source)
>                 at java.awt.EventQueue.access$200(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native

> Method)
>                 at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>                 at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native

> Method)
>                 at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>                 at java.awt.EventQueue.dispatchEvent(Unknown Source)
>                 at
> java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>                 at
> java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>                 at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>                 at java.awt.EventDispatchThread.pumpEvents(Unknown 
> Source)
>                 at java.awt.EventDispatchThread.pumpEvents(Unknown 
> Source)
>                 at java.awt.EventDispatchThread.run(Unknown Source)
> Caused by: java.sql.SQLException: File input/output error:
> java.io.IOException: Stream closed
>                 at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
>                 at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown

> Source)
>                 at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>                 at org.hsqldb.jdbcDriver.connect(Unknown Source)
>                 at java.sql.DriverManager.getConnection(Unknown Source)
>                 at java.sql.DriverManager.getConnection(Unknown Source)
>                 at
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)
>                 ... 58 more
> 
> I would greatly appreciate any assistance you might provide.
> 
> Alex

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